Have all sample names in samples
, one per line and run:
for sample in $(cat samples); do
IFS=$'\n'
for line in $(./sra-runs.py $sample); do
echo $sample $line >> runs
done
#!/usr/bin/env python | |
# install imagesize: pip install imagesize pyyaml | |
__author__ = 'Olivier Pieters' | |
__author_email__ = 'me@olivierpieters.be' | |
__license__ = 'BSD-3-Clause' | |
import yaml, imagesize | |
from os import listdir, rename |
/* | |
For any 1<k<=64, let mask=(1<<k)-1. hash_64() is a bijection on [0,1<<k), which means | |
hash_64(x, mask)==hash_64(y, mask) if and only if x==y. hash_64i() is the inversion of | |
hash_64(): hash_64i(hash_64(x, mask), mask) == hash_64(hash_64i(x, mask), mask) == x. | |
*/ | |
// Thomas Wang's integer hash functions. See <https://gist.github.com/lh3/59882d6b96166dfc3d8d> for a snapshot. | |
uint64_t hash_64(uint64_t key, uint64_t mask) | |
{ | |
key = (~key + (key << 21)) & mask; // key = (key << 21) - key - 1; |
#!/usr/bin/env python | |
""" | |
Convert camel-case to snake-case in python. | |
e.g.: CamelCase -> snake_case | |
e.g.: snake_case -> CamelCase | |
e.g.: CamelCase -> dash-case | |
e.g.: dash-case -> CamelCase | |
By: Jay Taylor [@jtaylor] | |
Me<modifier>: Yahya Kacem <fuj.tyoli@gmail.com> | |
Original gist: https://gist.github.com/jaytaylor/3660565 |
""" | |
Example for a colourised logging output. | |
This example uses "blessings" to handle console escape sequences. ``blessings`` | |
itself is a very harmless package in that it does not have any external | |
dependencies. And it's code-base is very clean and small. | |
The example extends the core logging formatter (logging.Formatter) and | |
colourises the complete line. This takes advantage of any upstream updates | |
related to logging. When writing this against Python 2.7, the parent code |
rsync (Everyone seems to like -z, but it is much slower for me)
Arg Name or Optional Flags: | |
positional : str = "foo" | |
options : str = "-f", "--foo" | |
Standard: | |
action : str = [store], append, store_true, store_false, store_const, append_const, version | |
default : * = [None] | |
type : callable = [str], argparse.FileType(mode='wb', bufsize=0) | |
Exotic: |